FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa

The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum

Humanity will always be indebted to plants. In the ongoing scientific era, the 'Herbal Revolution' has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.

DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development

An updated (and now online) version of the former chromosome database of tribe Delphinieae (Ranunculaceae) is presented ( http://www.delphinieae.online ). This new version is the result of an accurate, exhaustive literature and Internet research, by adding chromosome counts and all related karyological information for the genera Aconitum L., Gymnaconitum (Stapf) Wei Wang & Z. D. Chen, Delphinium L. (including Staphisagria Spach), Consolida (DC.) S. F. Gray and Aconitella Spach, accumulated during the approximately last 25 years and that comprise worldwide published data from 1889 to 2021. The Delphinieae Chromosome Database (DCDB) (last updated 31.12.2021) contains a total number of 3435 reports belonging to 425 species (503 taxa), which represents 48.6% of the total species of the tribe (an increase of c. 213% and 32% compared with the 1097 and 2598 reports gathered in the 1999 and 2016 versions, respectively). This increase is due both to chromosome research progress and to improved information capture system. Moreover, recent taxonomic advances, synonymization, and new phylogenetic criteria have also been considered.The DCDB database provides the most complete currently available information on published chromosome numbers, ploidy-level estimates, and other karyological data of Delphinieae, and it is aimed to be useful for the building of cytotaxonomical databases and for specific research ongoing projects of systematics and evolution of Ranunculaceae. DCDB includes two levels of taxonomic resolution, published name (original and standardized form) and database accepted name (based on either Plants of the World - POWO or expert specialist criteria), as well as the geographic origin of each count (country, locality, geographic coordinates, elevation, or ecological information when reported in the original publication), associated karyological data if originally provided (studied material type, graphic information, chromosome measures and formulas, satellites, B chromosomes, other cytogenetic techniques used, etc.), voucher information and reference (with DOI and other links to access the original document). An effort to check the original sources and to search in grey literature allowed to indicate the counts that appear to be registered twice.

Chromosomal view of Lippia alba, a tropical polyploid complex under genome stabilization process

Lippia alba is a phenotypically variable tropical shrub thought to comprise a young autopolyploid complex. Chromosome numbers in L. alba include 2n = 30, 38, 45, 60, and 90. High levels of chemical and phenotypic variation associated with economic and medicinal importance were reported. However, the genetic background including chromosome composition remains under-explored. Furthermore, the occurrence of at least four ploidal levels in L. alba and the lack of data for polyploid plants in tropical areas also merit further study of L. alba. Here we assessed the chromosome composition using two new satellite repeats (CL98 and CL66) applied as FISH probes to mitotic chromosomes, and we proposed to calculate the degree of homozygosis for CL66 satDNA (named as index h) and to associate it to meiotic instability. The CL98 mapping showed few variations in both number of signals and position. However, the levels of structural homozygosity for a satellite repeat CL66 were very variable. The numbers of CL66-bearing-chromosomes were under-represented in tetraploids relative to diploids implying that CL66 arrays have been lost in tetraploid lineages as a result of increased meiotic instability. High percentage of irregularities was observed in meiotic cells, especially in polyploids. L. alba complex comprised a mixture of homomorphic and heteromorphic chromosomes. Overall, the polyploid complex presents features typical of both young and older stable polyploids. It seems that L. alba genome is still in the process of stabilization.

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

INTRODUCTION

Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.

RESULTS

(i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures.

CONCLUSION

We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.

Comparative karyotype analysis among six species of Ipomoea based on two newly identified repetitive sequences

Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of Ipomoea (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, and I. × leucantha) and understand the relationship among these species. Two satellite repeats (viz., Itf_1 and Itf_2) were identified from the diploid I. trifida genome sequence using RepeatExplorer on Galaxy. Together with the ribosomal DNA (rDNA), although without distinguishable chromosomes, a detailed karyotype was constructed for the six species. Our results showed a similar karyotype between I. tenuissima and I. × leucantha, indicating their close relationship. The signal distribution pattern of Itf_1, 45S rDNA combination, detected only in I. trifida, I. tabascana, and I. batatas, implied their close relationships. The chromosomes carrying 5S rDNA could be conserved among the six species as they always carried the Itf_2 signals, which generated a similar signal distribution pattern. The results enabled a detailed comparative cytogenetic analysis, providing valuable information to understand the relationship among these species and help assemble the genome sequence of the six species of Ipomoea.